Bioinformatics Clemson Exam 1

Which database is best to search and retrieve biomedical literature information?

PubMed

GenBank

Contains an annotated collection of all publicly available DNA sequences

Hidden Markov Models include...

GENSCAN, FGENESH, AUGUSTUS

The Gene Ontology (GO) consists of three unlinked hierarchies, which are...

MF, BP, CC

Molecular Function, Biological Process, Cellular Component

Foreign Key

-an attribute in one table and the primary key of another table

-used to establish a link between the data in the two tables.

What BLOSUM and PAM numbers are best for working with distantly related sequences?

Higher [PAM] and lower [BLOSUM] numbers

What does the definition line start with in FASTA format?

>

What do scalar variables begin with in FASTA format?

$

What percent of the human genome consists of repetitive elements?

50%

UniGene

provides a non-redundant set of gene transcripts for an organism

UniProt contains contains data resource including...

Swiss-Prot, TrEMBL, and Proteomes

Example of database federation

NCBI

What are the three terms used in SQL to retrieve data?

SELECT>FROM>WHERE

RefSeq

provides high-quality (curated by experts), comprehensive, non-redundant set of sequences

Which database is best for information on human diseases?

OMIM

Genome browsers developed to facilitate human genome annotation

Ensembl, NCBI Map Viewer, UCSC Genome Browser

What symbols can variables start with in PERL?

-$

-@

-%

-#

-a number

$ and @

In the three-tier architecture of a database system, the database tier...

Handles data storage and queries

In the three-tier architecture of a database system, the interface tier...

Interacts with users so they can obtain data- web interface

In the three-tier architecture of a database system, the application tier...

is constantly changing, new tools/programs can be developed or added anytime

-database connection

UniProt KB

-good database for protein sequences

UCSC Genome Browser

-organizes data into tracks that can be displayed or hidden by the user

-supports text-based queries and BLAT

What does an extremely small E-value mean for homology?

-the lower the value, the more significant

-a very small value means they are definitely similar sequences

-therefore, the target sequence is a candidate for homology, but more proof is still needed

PSI-BLAST

works by constructing a PSSM to facilitate the search

Relational Data Model

organizes data into relations (tables)

Primary Key

-chosen to represent the most essential information in the table